From 25a2da2b52a5e46e1b726a28786e37ec426681ec Mon Sep 17 00:00:00 2001 From: fraser-combe Date: Mon, 4 Nov 2024 10:13:54 -0600 Subject: [PATCH] update flu output --- workflows/utilities/wf_flu_track.wdl | 14 +++++--------- 1 file changed, 5 insertions(+), 9 deletions(-) diff --git a/workflows/utilities/wf_flu_track.wdl b/workflows/utilities/wf_flu_track.wdl index 13c6bc36e..6a2b9fd9b 100644 --- a/workflows/utilities/wf_flu_track.wdl +++ b/workflows/utilities/wf_flu_track.wdl @@ -112,16 +112,12 @@ workflow flu_track { docker = assembly_metrics_docker } } - # Calculate the percentage of mapped reads for flu samples - if (defined(irma.seg_ha_bam) || defined(irma.seg_na_bam)) { - call assembly_metrics.stats_n_coverage as flu_stats_n_coverage { - input: - samplename = samplename, - bamfile = select_first([irma.seg_ha_bam, irma.seg_na_bam]) - } - } # combine HA & NA assembly coverages String ha_na_assembly_coverage_string = "HA: " + select_first([ha_assembly_coverage.depth, ""]) + ", NA: " + select_first([na_assembly_coverage.depth, ""]) + + # combine HA & NA mapped reads percentages + String ha_na_mapped_reads_percentage_string = "HA: " + select_first([ha_assembly_coverage.percentage_mapped_reads, ""]) + ", NA: " + select_first([na_assembly_coverage.percentage_mapped_reads, ""]) + # ABRICATE will run if assembly is provided, or was generated with IRMA if (defined(irma.irma_assemblies) && defined(irma.irma_assembly_fasta)){ call abricate.abricate_flu { @@ -264,7 +260,7 @@ workflow flu_track { File? irma_na_bam = irma.seg_na_bam String ha_na_assembly_coverage = ha_na_assembly_coverage_string # calulate mapped reads percentage for flu samples - Float? percentage_mapped_reads = flu_stats_n_coverage.percentage_mapped_reads + String percentage_mapped_reads = flu_stats_n_coverage.percentage_mapped_reads # GenoFLU outputs String? genoflu_version = genoflu.genoflu_version String? genoflu_genotype = genoflu.genoflu_genotype